Abstract Proceedings of the 7th International Congress of the Molecular Biology Association of Turkey: İstanbul, Turkey. 27-29 September 2019.

Results: Resveratrol and its combinations significantly induced apoptosis except combinations with myriocin and also caused cell cycle arrest at different phases and modulated the expression of BCRABL. Resveratrol modulated sphingolipid metabolism by altering the expression of key enzymes based on the cell type studied. Conclusion: Resveratrol modulated the expression of key sphingolipid enzymes involved in leukemia development and BCR-ABL. Combination of resveratrol with the inhibitors of sphingolipid enzymes could be a new approach for the treatment of Ph+ ALL.

• Contribution is open to researchers of all nationalities.
• Letters to the editor reflect the opinions of other researchers on articles published in the journal.
• The editor may invite survey reviews concerning recent developments in particular areas of interest. The annual MolBiyoKon congress is organized by the Molecular Biology Association of Turkey and is one of the primary and noteworthy international conferences in the field of molecular biology in Turkey. The congress aims to bring together scientists from all around the world to disseminate research results and exchange ideas, as well as to motivate and inspire students to pursue their careers and education in the life sciences.
This year's congress hosts 15 international speakers and 15 speakers from Turkey. There are more than 450 participants from different backgrounds and practices of life sciences. The congress covers diverse topics, including but not limited to bioinformatics, omics technologies, molecular medicine, metabolic regulation, developmental biology, protein dynamics, macromolecular assemblies of the cell, and biological drug development. There are also two poster presentation sessions and a discussion panel on personalized medicine.
We thank all participants, speakers, sponsors, the Turkish Journal of Biology, and those involved in the organization for their contributions in making this congress an exciting and fruitful one.
On behalf of the organizing committee, Assoc. Prof. Gizem Dinler Doganay liver. No drug has been identified for the specific treatment of anti-metastasis in HCC. The drugs used in the treatment of primary HCC tumors are similar to the ones used against tumor metastasis.
Cisplatin, doxorubicin and 5-FU are members of these cytotoxic drugs. The EGFR pathway plays an important role in promoting HCC metastasis, although the mechanism remains unclear. A cholinergic system with acetylcholinesterase and acetylcholinic receptors has been detected in HCC although the function and molecular mechanism in hepatic carcinogenesis are unknown. The aim of this study is to investigate the role of EGFR-AChR signaling pathway on cell proliferation in HCC. In addition, this study showed that the exposure of human HepG2 hepatoma cells to palmitate results in apoptosis.
Marmara University, İstanbul, Turkey Intramuscular drug application in zebrafish Background/aim: Zebrafish (Danio rerio) is a freshwater fish that constitutes a convenient vertebrate model for the study of many disorders because it has a genetic structure to humans highly similar. It became a useful tool in drug treatments recently. Drug delivery in zebrafish adults can realize with small molecules by means of water-borne exposure, use oral gavage or injection techniques. In this study, we delivered a drug directly wild-type zebrafish adults muscles via intramuscular injection to standardize the intramuscular drug administration protocol to be applied to zebrafish adults. Besides, we created muscular dystrophy phenotype in the zebrafish model the LGMD2R (MIM 615325/Orpha code: 363543) phenotype caused by DES mutation. So, we also will use this method in desma mutant zebrafish adults. Aims of this study are both setting up convenient intramuscular drug application algorithm for zebrafish adults and investigating whether relieving the muscle dystrophy phenotype caused by the mutation or not.

Abstract
Background/aim: Phospholipase A2s (PLA2)s are lipolytic enzymes hydrolyzing membrane phospholipids to form fatty acids and lysophospholipids. One of the key products is Arachidonic Acid (AA) that can be metabolized into prostaglandins and leukotrienes. sPLA2s have been associated with various cancers including prostate cancer. High level of sPLA2-IIA is correlated with high prostate tumor grade, tumor proliferation in primary site tumors. The expression of sPLA2-IIA both in mRNA and protein level increases more rapidly in metastatic tumors when compared to benign tumors. Furthermore, clinical studies on different single nucleotide polymorphism (SNP) of sPLA2-IIA indicated an association between the elevated serum levels of sPLA2-IIA in the cancer patients of afore mentioned diseases.

Materials and methods:
Possible effects of missense variants were investigated through molecular dynamics simulations. For this purpose, mutated proteins were modelled in Cyrus Bench and simulations were run in Amber12 software. Results have been investigated in terms of H-bonding and surface electrostatic potential change. Genetic profile from a total of 267 blood samples (82 control and 184 PCa) was analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method and Sanger sequencing.

Conclusion:
Our results showed that although there is a strong association between heterozygous genotype of rs11573156 (p<0.05) and prostate cancer, there is no association between other missense variants and prostate cancer.

Association of single nucleotide polymorphisms (SNP)s in PLA2G2A gene with prostate cancer
This study aims to investigate the association of 5'UTR variant rs11573156 and the missense variants rs374105365 and rs965800220 on prostate cancer development.
Results: Two missense variants, rs374105365 and rs965800220, show no effect on catalytic dyad interaction in terms of H-bond profile, while changes in amino acid side groups caused shift on surface electrostatics. The heterozygote allele of rs11573156 shows a 2-fold decreased risk for PCA while no significant correlation was detected for other SNPs.

Detecting CNVs in Hereditary Cancer: Is there an alternative for MLPA?
Nihat Buğra AĞAOĞLU 1,* , Gizem ALKURT 2 , İzzet Mehmet AKÇAY 2 , Elifnaz ÇELİK 2 , Jale YILDIZ 2 , Kübra ERMİŞ TEKKUŞ 1 , Sezin CANBEK 1 , Gizem DİNLER DOĞANAY 2 , Levent DOĞANAY 2 *Correspondence: nbagaoglu@hotmail.com Abstract Background/aim: Cancer is a disease that related to both genetic and environmental factors. Various genetic disorders may cause susceptibility to cancer as copy number variations (CNV). Many publications reveal the relationship between CNVs and the development of breast and colon cancer. MLPA (Multiplex Ligation-dependent Probe Amplification) is widely used to detect CNVs in breast and colon cancer cases. Recently with developing of the new algorithms in NGS data analysis, deletion/duplication detection can be performed in NGS data.

Materials and methods:
Peripheral blood samples obtained from the patients were tested by MLPA and NGS methods in germline samples for deletions/duplications after wet laboratory procedures in our laboratory.
Results: NGS and MLPA data were compared in 258 patients. In 247 of these patients, no deletion/ duplication was detected in CNV analysis of NGS data. This result was consistent with the results of MLPA analysis in the same patients. In 7 patients, the same germline pathogenic variation was detected in both NGS and MLPA data. MLPA and NGS test results were discordant in 4 patients.

Conclusion:
Our study suggests that the reliability of the algorithms currently used in the detection of CNV from NGS data is not yet sufficient for routine diagnosis and that the results need to be confirmed by MLPA. Further studies are necessary in the field of developing algorithms.

Key words: Cancer, Copy Number Variation, Multiplex Ligation-dependent Probe Amplification, Bioinformatics
In Umraniye Training and Research Hospital GLAB, molecular genetic tests have been performed for 750 breast cancer and 250 colon cancer patients to detect hereditary cancer syndromes. In the NGS data of 390 breast cancer and 125 colon cancer patients. CNV analysis was performed with Sophia DDM bioinformatics software algorithm. The obtained data were compared with MLPA analysis performed in 258 of them.
Statistical analyses were performed by GraphPad Prism version 8.0.1.

Results:
Autophagy markers were significantly upregulated in 3 to 6 hours of starvation in BT-474 cells. Serum starvation of the cells resulted in increased levels of p-Beclin 1 (T119), and conversely, decreased levels of p-Bcl-2 (S70) within this time period. BAG-1 levels, especially BAG-1S isoform, were started to increase after 6 hours of treatment.

Conclusion:
We conclude that autophagic response is induced between 3 to 5 hours of serum starvation in BT-474 cells. Disruption of Bcl-2/Beclin 1 interaction likely occurs through phosphorylation of Beclin 1. The increase in BAG-1 levels at the end of autophagic flux suggested that BAG-1, in particular BAG-1S isoform, may have a role in tipping the balance toward proteasomal activation.

Abstract
Results: Only single TK-pool, consisting of PTK2B, PTK6, ZAP70, NTRK3 was able to rescue growth in MEFs upon p110α/β dual-loss. In proliferation assays, activated ZAP70 expression compensated growth deficiency in PI3K inhibited MEFs and significantly elevated growth rates of MCF10A. ZAP70 synergized with HRAS-G12 for transformation of MEFs on soft agar. ZAP70 expressing RPE1-hTERT cells proliferate at faster rate and became more resistant to p110α inhibition in comparison to controls.

Conclusion:
Besides having critical functions in immune system, ZAP70 may be potent driver of proliferation and transformation in epithelial as well as mesenchymal cells upon PI3K abrogation. Therefore studies on ZAP70 mediated growth in solid tumors is warranted.

Materials and methods:
We have TK library consisting of 73 kinases, have C-terminal dimerization tags promote trans-phosphorylation for constitutive activation. Genetically engineered MEFs, where PI3K signaling can be abrogated upon Cre-expression, was used for screening the library. To mimic p110α/β catalytic inactivation in MEFs, pharmacological inhibition that we employed p110α/β inhibitors BYL719/KIN193, has been used in addition to genetic knock-outs.For conditional knockout of p110α/β, Adenoviruses expressing Cre-recombinase recognize lox-P sites inserted within first exons of PIK3CA-PIK3CB were used. Cell viability was assessed using crystal violet staining. To check anchorage independent growth and transformation ability of TKs of interest, soft agar growth assays were performed. We executed these experimental procedures for MEFs, MCF10A,RPE1-hTERT. cellular signaling. PI3K (Phosphoinositide 3-Kinase) is the most deregulated pathway in human cancers, activated via oncogenic Ras/receptor tyrosine kinases (RTKs). High levels of tyrosine phosphorylation associated with proliferation, which is regulated by PI3K.We are investigating whether tyrosine kinase contributes to growth compensation in response to p110α/β inhibition todemonstrate potential modes of resistance to PI3K targetted therapies.

The effects of Maackia amurensis leukoaglutinin on the alternative splicing events of human anaplastic thyroid cancer cell 8505C
Results: Our results showed that MAL treatment significantly affected alternative splicing events of 832 mRNA. The differentially spliced mRNAs grouped in protein class category were mostly involved in nucleic acid binding which included 14.1% of the mRNAs.

Conclusion:
Overall findings have suggested that MAL treatment affects alternative splicing events in human anaplastic thyroid cancer cells. Differentially spliced 117 genes have indicated that the MAL treatment affects transcriptional processes in the cells. Consequently, the alternative splicing events can be an important factor in the suppression of malignant and tumorigenic properties of 8505C cells when considering our previous findings.
Background/aim: Many variations in the transcriptome play a role in the biogenesis, progression and metastasis of cancer cells. The splicing process generally deteriorates in cancer cells and this phenomenon is resulted in both functional and non-functional end products. Protein isoforms arising from alternative splicing of many genes have been associated with various aspects of cancer formation and progression. Our previous study has shown that Maackia amurensis leukoagglutin-II (MAL) decreases the tumorigenic and malignant characteristics of 8505C human anaplastic thyroid cancer cells. In this study, it was aimed to evaluate how differential splicing events are affected by MAL treatment to 8505C cells by using RNA-Seq data, which allows the identification of alternative splicing isoforms.

Materials and methods:
Differential alternative splicing events were analysed using Illumina next generation sequencing technology by using cDNA libraries obtained from total RNA isolates of 8505C cells treated with 0.25 µM MAL-II for 24 hours. We also performed functional enrichment analysis of the differentially spliced mRNA and they were grouped based on protein class using PANTHER resource.
predominantly (~5%) in High-Density Lipoprotein (HDL) and in trace amounts (<2%) in Low-Density Lipoprotein (LDL). ApoM plays important role in HDL metabolism via reverse cholesterol transport and has protective effects against LDL oxidation and atherosclerosis. Clinical studies revealing the association between ApoM and diseases are very limited. Therefore, we aimed to investigate the relationship between serum ApoM and lipid levels in restenosis patients and healthy controls. This is the first study investigating the association between serum ApoM and lipid levels in restenosis patients.

Conclusion:
Serum apoM level exhibited a significant, positive correlation not only with the HDLcholesterol level, but also with the TG and LDL-cholesterol levels in patients with restenosis. These results indicated that the serum ApoM levels may affect the serum TG and cholesterol levels so that contributes to the development of restenosis.

Eosinophil-like EoL-1 cells
Ilgın AKKAYA, İrem OZEL, Onur ESKIOCAK, Ceren CIRACI * *Correspondence: ciracic@itu.edu.tr Abstract Background/aim: Histone Deacetylase inhibitors (HDACi) have been reported to have complex immunomodulatory properties, particularly by negatively regulating the Toll-like receptor (TLR) pathways in different immune cells through histone modification and regulation of the chromatin structure. Nonetheless, the effects of HDACi in the regulation of eosinophilic, allergic functions and cytosolic NOD-like receptors (NLRs) are unknown. Henceforth, we aimed to investigate the immunomodulatory roles of HDACi in eosinophil-like cells and whether they have specific roles in shaping the functionality of NLRs.

Materials and methods:
To investigate the effects of HDACi in regulating eosinophilic functions and NLRs, EoL-1 cells were stimulated with valproic acid (VPA), romidepsin and sodium butyrate. mRNA levels of TLRs, NLRs, eosinophil specific anti-inflammatory receptor Siglec-8 and allergyrelated Fc Epsilon receptors were analyzed by RT-qPCR. Protein levels of NLRs and TLRs were determined by immunoblotting. Flow cytometry experiments were performed to analyze the surface expression of Siglec-8 and Fc epsilon receptors. To determine the effects of HDACi on IL-1B and IL-6, ELISA experiments were utilized.

Results:
HDACi treatment drastically downregulated the expression of NLR proteins at mRNA and protein levels. This pattern was not observed in TLR protein expression although TLR mediated IL-6 secretion declined after HDACi treatment. Interestingly, HDACi treatment did not alter the surface expression of Siglec-8 or the Fc Epsilon receptors.

Conclusion:
This study demonstrated the specific downregulation of NLRs in EoL-1 cells while TLR expression was not diminished. Furthermore, HDACi reduced the secretion of IL-6, a downstream product of the TLR pathways. Our data present possible targets in the regulation of NLR expression which can lead to the characterization of new molecular mechanisms of eosinophilic and allergic functions. to cytoskeleton defects, especially in neurons, due to dysregulations in regulatory proteins. Our previous results showed impaired microtubule stability in SMN depleted cells and also alterations in some microtubule associated proteins, including microtubule-associated protein 1B (MAP1B).

End-binding 3 protein alterations in an in vitro spinal muscular atrophy model
MAP1B affects the activity of microtubule plus-end protein, end-binding 3 (EB3), via regulating its microtubule binding. Therefore, in this study, we investigated the expression and localization of EB3 proteins in an in vitro SMA model.

Results:
We detected a significant downregulation in EB3 protein level in SMN knock down cells.
We also found that comet numbers were significantly increased at the beginning of neurites, however, the area of one comet on dynamic microtubules was reduced.

Abstract
Background: Cancer is one of the highest rated disease on the values of mortality ratio. Among several types of treatment options, chemotherapy is still the most used. Cytotoxic drugs are widely used against cancer during chemotherapy. However, the drug efficacy might be interfered when cancer cells develop resistance to these drugs. This resistance may occur by several different reasons such as cancer heterogenity, molecular changes, drug efflux, etc.

Material/Method:
In our experiments, we used doxorubicin as a model drug. Dox is a topoisomerase II poison that causes DNA double strand breaks. Thus, on fast dividing cells, such as cancer cells, dox has a cytotoxic effect because cells cannot keep up repairing these breaks. We planned to systematically knock out almost each protein coding gene in human MDA-MB-231 cancer cell line in order to screen the contribution of their individual absences in developing resistance to doxorubicin.

Result:
We isolated their genomic DNA, PCRed out the integratad viral genome sequences. Later we sequenced the PCR product on next generation sequencing platform and the results are in the progress of analysing the data.
Conclusion: By this, we will identify the mutant genes that confer resistance to cancer cells. The products of the identified genes might have potential to be targets for new diagnostic tools and therapy approaches for cancer in clinics.
Keywords: CRISPR/Cas9, gene editing, drug resistance, breast cancer, chemotherapy This project is supported by TUBİTAK 1003, grant number: 216S404 1 Acibadem Mehmet Ali Aydinlar University, İstanbul, Turkey Busra GUNAY * , Ebru GONCU *ozerbusra54@gmail.com Abstract Background/aim: Autophagy is thought to be a critical mechanism for providing self-renewal, proliferation and differentiation of stem cells. Bombyx mori midgut enters remodelling process during larval-pupal metamorphosis. Larval midgut stem cells undergo growth, proliferation, and differentiation, which leads to the formation of the pupal epithelium. In this study, the role of autophagy mechanism in stem cells forming pupal midgut was investigated.

Conclusion:
As an autophagy inhibitor, chloroquine regulates the breakdown of autophagic protein in the lysosomal system. In this study, after chloroquine application, increasing expression of autophagy-related genes, increasing acid phosphatase enzyme amount and abnormal morphological findings, indicated the role of autophagy in the proliferation and differentiation of midgut stem cells.

Materials and Methods:
In order to prevent autophagic activity, the larvae were administrated chloroquine by injection in two different doses, 1 mg and 3 mg, on days 7 and 8 of the fifth instar.
Stem cells were isolated from midgut in every 24 hrs. The expression levels of autophagy-related genes ATG8 and ATG12 in stem cells were determined by qRT-PCR. The amount of lysosomal enzyme acid phosphatase was measured spectrophotometrically. Proliferation and differentiation of stem cells were also investigated morphologically. The findings were evaluated comparatively with the control groups.
Results: Metamorphosis did not occur in silkworms treated with chloroquine. In the control groups, ATG8 and ATG12 mRNA levels increased on days 8 and 9, and continued to decrease until 24 th hour of pupa. On day 8, except for 3 mg of chloroquine treated group, significant increases in the expression of the genes studied in the other treatment groups were observed. Acid phosphatase enzyme increased in stem cells immediately after application of chloroquine. In the results of morphological analysis, chloroquine applications prevented differentiation of stem cells and healthy organization of pupal epithelium.
Ege University, İzmir, Turkey Abdullah Gul University, Kayseri, Turkey *Correspondence: oktaykaplan@gmail.com Abstract Background/aim: Determining the biological impact of the ever-increasing number of human genetic variants is presently challenging. The functional inference computational tools are apparently not adequate enough for predicting functional consequences of missense variants, requiring experimental evaluation of these variants. CRISPR/Cas9 technology is a cost-effective and a rapid method to introduce a single nucleotide change to any part of genome. By employing CRISPR/Cas9 technology, we investigated the biological functions of two variants (P726A and G704S) in short-rib thoracic dysplasia associated IFT140 (Intraflagellar Transport 140) gene in C. elegans.

Materials and methods:
ConVarT (www.convart.org), a new tool developed by our research group, was used to find two conserved variants between human and C. elegans with high pathogenic score.
Homozygous mutants carrying a single amino acid change (IFT140 P726A or IFT140 P726A ) in C. elegans were generated using the CRISPR/Cas9 system. Dye filling assay and microscopic analysis were used to assess functional effects of these variants on the structure of cilia.

Results:
Although both variants are predicted to be pathogenic by functional prediction programs, SIFT and PolyPhen-2, we have found that IFT140 P726A , but not IFT140 G704S mutant phenocopies IFT140 null mutant for the ciliary accumulation of IFT proteins and short cilia. The IFT140 P726A phenotype was fully rescued by introducing wild type IFT140. İstanbul University, İstanbul, Turkey 1 Abdullah Gül University, Kayseri, Turkey

Contact with senescent mesenchymal stem cells (MSCs) modulate secretome composition
Background/aim: Aging is one the largest risk factor for the onset of cancer which could be to certain extent a consequence of the increased senescent cells during aging. Senescent mesenchymal stem cells (MSCs) secrete signals known as "senescence-associated secretory phenotype" which could modify their microenvironment and contribute to cellular proliferative arrest. We previously showed that once the senescent MSCs contacted with myeloma cells, myeloma cells can manipulate senescent MSCs secretome and impair their anti-proliferative activity to survive and grow. Cancer cells might secrete molecules that manipulate the secretome content of MSCs. In order to elucidate this interaction, we aimed to investigate the secretome of myeloma cells.
profoundly modified by the direct interaction with senescent MSCs. Globally, direct priming induced the production of 129 proteins and repressed the secretion of 67 others. However indirect priming had very little effect on cancer cell secretome.
result suggest that mesenchymal stem cells more efficiently. Further investigation on pathways and signalling molecules needs to be done.

A candidate gene obtained from methylation/expression arrays showed methylationindependent expression loss in oral carcinoma
Semra DEMOKAN * , Onder ERYILMAZ, Sevde COMERT, Sena SEN, Murat ULUSAN *Correspondence: demokan@istanbul.edu.tr Abstract Background/aim: In our study (supported by TUBITAK-SBAG-114S497), we aimed to investigate the potential epigenetic biomarker candidate genesobserved methylation-dependent expression loss via methylation and expression array methods in oral squamous cell carcinoma (OSCC) patients. Results: After bioinformatic analysis, we identified 409 candidate genes using specific probes detecting methylated the CpG regions in the tumor groups compared to matched-normal groups, while the decreased expression levels in tumors were observed in 35 genes. From those data set, we were searching epigenetic candidate biomarker genes observedmethylation-dependent expression loss. A candidate gene from this gene panel showed significant hypermethylation and decreased expression levels, and it was choosing to perform further validation in a larger patient cohort. The decreased expression levels of this candidate gene (unpublished data) that play an important role in the cell adhesion processes, was observed in 50% (10/20) of tumor samples compared with matched normal tissue, whereas the expression levels were increased in Conclusion: We concluded that hypermethylation may not the suppression mechanism for this gene's decreased expression. The methylation results of the array cohort and the validation cohort was different since the patients were not the same in both groups. The decreased expression levels of this candidate gene may be associated with the carcinogenesis mechanism of oral cavity.

Material and methods:
İstanbul University, İstanbul, Turkey Bursa Uludag University, Bursa, Turkey *Correspondence: dilekpirim@uludag.edu.tr Abstract Background/Aim: Accumulating evidence indicates the value of utilizing miRNAs as a biomarker for Schizophrenia (SCZ), however their potential functions in the SCZ pathogenesis are largely unknown. The aim of this study to identify putative functions of miRNAs in molecular networks and assess their interactions with key regulators contributing to the SCZ-associated pathways by using bioinformatic tools.

Materials and Methods:
Microarray data set (GSE54578) was downloaded from Gene Expression Omnibus. Differentially expressed miRNAs (DEMs) were analyzed in GEO2R using Limma R and the cut-off criteria for DEMs were set as an adjusted-p<0.05 and a fold change>1.5 or <-1.5. DIANA miRPath and DAVID databases were used for functional enrichments of the DEMs and their targets, respectively. Target genes of the miRNAs were analyzed by using Ingenuity Pathway Analysis and constructed protein-protein interaction was imported to Cytoscape for visualization and hub gene identification. Transcription factor (TF)-miRNA interactions were also assessed by Transmir and expressions of the possible hub genes were evaluated in SCZ patients and healthy individuals through schizophrenia database (SZDB).
Results: A total of 18 DEMs were found in SCZ patients as compared to controls. Top Kyoto Encyclopedia of Genes Genomes (KEGG) category was related immune system (chemokine signaling pathway). Functional enrichment of significant DEMs revelaed several significant pathways highlighting their roles in glycan metabolism, substance addiction and cancer. Seven hub genes were identified by Cytohubba and evaluating them in SZDB revealed AKT1 and PI3K were dysregulated in SCZ. TP53, one of the hub gene, was the top transcription factor that was predicted to be regulated by 10 miRNAs in TF-miRNA interaction analyses.

Conclusion:
Our results highlight candidate molecular pathways and key regulators that may involve in the etiology and pathogenesis of SCZ of which can be utilized to further elucidate the SCZ susceptibility and management.

Materials and methods:
We purified the ASC specks particles carrying antigenic epitopes and evaluated their properties as novel adjuvant/carrier to achieve immunity in C57/BL6 mice as model for tumor eradication or immunity against viral infections.
Results: After stimulation of macrophages driven from THP-1 cells we showed an increase in secretion of certain inflammatory cytokines including IL-1 beta and TNF alpha. Furthermore, C57BL/6 mice vaccinated with tH5-ASC specks showed higher IgG level in comparison to those receiving to those vaccinated by alum adjuvanted or non-adjuvant antigen. Lastly, we showed that animals immunized Upon stimulation, ASC combine into large filamentous structures which eventually came together forming a globular structure also known as the ASC-speck. These specks might remain inside the cells or can be released into extracellular matrix and amplify the inflammatory response. Our group previously showed that ASC specks can artificially be loaded with antigens and these, antigen loaded particles can remain stable at 37°C at least for a month. Also, in In vivo model after intra-peritoneal injection ASC specks tend to accumulate in the spleen with relatively long-lasting stability.
Dysregulation of Erbin can lead to tumorigenesis. Breast cancer is one of the types of cancer that is affected by Erbin regulation. However, it is unclear how Erbin regulates the biological behavior and drug resistance of breast cancer cells. The main aim of our study is to explore the role of the Erbin gene in drug resistance in breast cancer.

Real-time and label-free evaluation of cellsurface interactions
İstanbul Technical University, İstanbul, Turkey The mutation spectrum of our patients with nephrological disorders Materials and methods: Patients admitted to our outpatient clinic from June 2018 to September 2019 with a symptom scale of hematuria, proteinuria, abdominal pain, renal cysts, nephrolithiasis.
There were 15 females and 10 males aged between 6 months to 35 years of age. The urinary system ultrasonography, urine analysis and biochemical examinations were evaluated for all of them.
For genetic analysis after peripheral blood DNA isolation and adapter application, we had amplified 33 genes associated with nephrological disorders. After sequencing at Illumina Miseq R platform the vcf files were analysed at Sophia DDM v.4 software. The mutations were analysed with uptodate databases for prediction of pathogenicity and classified according to ACMG guidelines. Segregation analysis and genetic counselling were performed with Sanger Sequencing for all families.

Results:
We have detected 25 mutations associated with disease phenotype. There were three patients with pathological mutation at more than one genes and one patient had two homozygous mutations at the same gene that one of them is pathological while the other was defined as variant of unknown significance (VUS). We had 3 Bartter Syndrome, 5 Polycystic Kidney Disease, 5 renal tubular acidosis, 5 Alport Syndrome, 1 Hyperoxaluria, 1 Recurrent Nephrolithiasis, 1 Hypophosphatemia, 1 Renal Agenesis, 2 Nephrotic Syndrome and 1 Wilm's Tumour patients whose diagnosis were confirmed genetically.
Marmara University, School of Medicine, İstanbul, Turkey Kaya İŞLEYEN, Filiz ERÇELIK, Emrah NIKEREL, Bahar SOĞUTMAZ ÖZDEMIR * *Correspondence: bahar.sogutmaz@yeditepe.edu.tr Abstract Background/aim: Enzymes are important macromolecules relevant for industrial production. High level expression of these enzymes is key for large-scale production. Recombinant DNA technology is used to produce tailor-made enzymes with increased expression level and yield. Signal peptides (SP) are short sequences that guide the produced enzyme to its final destination. Finding the suitable SP for the enzyme of interest directly affects the amount of secretion. However, an optimal SP for a protein can be predicted only upon an intensive screening. Phytase is a significant commercial enzyme that hydrolyze phytic acid to inorganic phosphate. Bacillus subtilis is able to express proteins extracellularly, therefore is a good candidate for SP optimization studies. The aim of the study is to produce extracellular phytase from B. subtilis RIK 1285 with signal peptide modifications. As a whole, engineering of TFBS and other components attracts increasing attention especially within synthetic biology context, as their optimization significantly improves the enzyme production. In this study, TFBS in promoters located upstream of differentially expressed genes (DEGs) in Aspergillus niger were scanned and several TFBS motifs were discovered to be further used for promoter tuning.

Materials and methods: Various
A. niger transcriptomics data were analyzed to find out DEGs include transporters, proteases, and other cellular proteins. 1000 bp upstream sequences of these genes were chosen as possible promoter regions and analyzed using MEME Suite (http://meme-suite. org/tools/meme) tool for discovery of TFBS motifs. Each dataset and the corresponding genes were analyzed separately and the most common TFBS motif was found. Finally, they were aligned to check for similarities in their sequences.

Results:
A collection TFBS motifs was obtained including common sequences such as CT-rich regions, key sequences for mRNA stability.

Conclusion:
This approach constitutes the basis of engineering of regulatory elements in promoter regions. Output of this research provides key information for further promoter tuning studies.

Keywords: Aspergillus niger, enzyme production, industrial biotechnology, transcription factors
Acknowledgement: Financial support for Filiz Erçelik via TÜBİTAK 2211-C Program is gratefully acknowledged.

Motif discovery for engineering transcription factor binding sites in Aspergillus niger
Yeditepe University, İstanbul, Turkey Barış SALMAN 1,2,* , Sibel Uğur İŞERİ 2 *Correspondence: baris.salman@gen-era.com.tr Conclusion: There is high demand for customized bioinformatics tools that could be used in the medical genetics area due to growing number of NGS based clinical genetic tests. Picus aims to help genome analysts in this concept via increased automation in ACMG/AMP criteria. genes that are involved in this rewiring. The aim of this study is to identify miRNAs that are involved in nutrient restriction mediated rewiring of metabolism in cancer cells.

Materials and methods:
We have subjected Caco-2 CRC cells to nutrient restriction by culturing these cells for 48h in a pre-optimized mix of low serum [1% fetal bovine serum (FBS) as opposed to 20% FBS], low glucose (0.1g/L as opposed to 1g/L) and low L-glutamine (0.2 mM as opposed to 2mM). Later, protein samples were collected from control and nutrient restricted cells. Then, autophagy and apoptosis induction was assessed with western blotting for the autophagy and apoptosis markers.
Results: Under nutrient restriction, Caco-2 cells were observed to undergo autophagy, as indicated by enhanced ratio of LC3II/I, beclin-1 levels and p62 levels, and apoptosis, as indicated by decreased procaspase-3 levels.

Conclusion:
These results showed that starved Caco-2 cells underwent autophagy. This confirms the well-known paradigm that cells under the stress of starvation frequently undergo autophagy, a form of "self-eating" that allows the cell to eliminate organelles and proteins as well as other cargos in order to cope with the stress.

Comparison of autophagy in Bombyx mori midgut tissue under starvation condition and metamorphosis
Tuğçe ERGIN * , Ebru GONCU Ege University, İzmir, Turkey *Correspondence: tugcee.erginn@gmail.com Abstract Background/aim: Autophagy is a well-known physiological process which is mainly activated under starvation condition and act as a type of cell death under certain conditions. The aim of this study was to investigate the differences between autophagy processes during starvation conditions and metamorphic remodeling period of midgut of Bombyx mori.

Materials and methods:
Bombyx mori larvae were reared until 5 th larval stage. Half of the larvae were starved from the beginning of the 5 th larval stage. The other group was reared under normal feeding conditions. Midguts from both groups were dissected every 24 hours. Expressions of autophagy-related genes -ATG8 and ATG 12-were detected by qRT-PCR. Lysosomal hydrolytic enzyme acid phosphatase activity was measured spectrophotometrically as an autophagy marker.
Midgut morphologies were evaluated with qRT-PCR and enzyme activity results.

Results:
The starved larvae survived until day 7 of 5 th larval stage. In the control group ATG8 expression gradually increased from day 0 to day 7 of 5 th instar but its expression was considerably low in starved insects especially after day 2 of 5th instar. Similar to ATG8, ATG12 mRNA levels were found higher than starved insects. Acid phosphatase activities were not significantly different in both groups. Midgut morphologies were consistent with other results.

Conclusion:
Larval midgut is the main site for digestion. According to our results, autophagy was not stimulated in the midgut of starved larvae, conversely it was inhibited compared with the control group. These results suggested that autophagy is not involved in cell's survival during starvation. In addition a previous study showed that digestive enzyme synthesis activity of midgut cells precede under starvation condition. Therefore it is thought that cells meet the energy needs from the fat body in order to survive and maintain their functions.
Key words: Autophagy, Bombyx mori, midgut, starvation or MGAT1 have greater proliferative and invasive capabilities compared to wildtype Huh7 cells, and when subcutaneously injected into NUDE/SCID mice resulted in larger tumor formation. In this study, we investigated BRI3 and MGAT1 as novel targets of the Wnt/β-catenin pathway and their involvement in hepatocarcinogenesis in vitro. We examined the RNA-Seq results of tumors derived from either BRI3 or MGAT1 overexpressing Huh7 cells compared to GFP overexpressing Huh7 cells and observed differential expressions of several genes. By selecting three genes for both BRI3 and MGAT1 based on their fold change and relevance to cancer, we proposed possible mechanisms of both BRI3 and MGAT1 contributions to tumorigenesis separately.

Materials and methods:
qRT-PCR and Western Blot analyses have been used to determine differential expressions of selected genes in either BRI3 or MGAT1 overexpressing Huh7 cells compared to control. Bioinformatic analysis using PRISM online tool has been carried out.

Results:
We verified differential expressions of selected genes for both BRI3 and MGAT1 separately and proposed a possible mechanism using both our data and previous studies.

Materials and Methods:
Brachypodium distachyon plants were exposed to drought stress by water withholding for 12 days at their vegetative stage under greenhouse conditions. Proteins extracted from collected leaves were analyzed using western blot for HSP90 and TGase expression.

Results:
Western blots showed that HSP90 protein expression increased approximately 7-fold whereas TGase protein level decreased almost 0.23-fold under drought stress.

Conclusion:
The protein expression levels, together with known mechanisms and PA interactions under drought stress, have unraveled the possibility of an indirect interaction between HSP90 and TGase in Brachypodium distachyon. This study highlights the importance of molecular mechanisms behind drought stress.

Abstract
Results: Activation of apoptosis resulted in 4 to 8-fold repression of GPD1 and CYC1 genes transcription, both under fermentative and respirative growth conditions. On the other hand, activation of autophagy differentially affects the expression of GPD1 and CYC1 genes. While GPD1 transcription is activated by 25% upon autophagy signal triggered by caffeine incubation, transcription CYC1 is repressed by 2-fold.

Conclusion:
The activation of apoptosis rapidly represses the transcription of the GPD1 and CYC1 gene. It seems that apoptosis and autophagy signaling might affect redox balance within the cells through the regulation of GPD1 transcription.
Keywords: Apoptosis, autophagy, redox balance, cytochrome C1, yeast Background/aim: Autophagy and apoptosis are two basic cellular processes that are activated under distinct cellular growth conditions. NAD-dependent glycerol-3-phosphate dehydrogenase, which is encoded by the GPD1 gene, is essential for the regulation of redox balance. Cytochrome c, isoform 1, encoded by the CYC1 gene, locates within intermembrane space functions as the electron carrier for mitochondrial functions. Cyc1 also has a function in the initial stage of apoptosis. The aims of this study are to investigate how apoptosis and autophagy signaling affects the transcription of GPD1 and CYC1 genes. We have also tested the involvement of protein kinase Hog1/MAPK11 in regulation of these genes during apoptosis and autophagy signaling.

Materials and methods:
To quantitate the expression levels of GPD1 and CYC1 genes, we have used the LacZ gene fusions of GPD1 and CYC1 genes that contain the entire promoter regions of these genes. To activate apoptosis, yeast cells grown in 60 mM acetic acid for 5 h. Autophagy signaling is activated by blocking the TOR pathway with 8 mM caffeine.

Biotechnological production of an allergenic lipid transfer protein from Morus alba pollen
Narmin AGHALAROVA, Narmin MİRZAMAMMADLİ, Yunus AKSÜT, Nazlı ARDA * Conclusion: Obtained recombinant allergen may be used in the diagnosis and/or treatment of cypress allergy after clinical trials in the future. This study is expected to provide a basis to similar attempts to improve the sensitivity and reliability of diagnosis of allergic diseases, and success of treatment in patients living in İstanbul.  In order to map ubiquitin modified lysines on Cas9 proteins we prepared samples for LC-MS/MS and sent them to EMBL for analysis.

Methylation and expression levels of
Results: All cell biology-based techniques (His-pulldown, IP and PLA) showed strong ubiquitylation on Cas9 protein. Several lysines were mapped to be ubiquitylated by mass spectrometry.

Conclusion:
We expect that these results will lead to a better understanding of the eukaryotic posttranslational regulation of Cas9. Our hope is that uncovering the functional implications of these PTMs will contribute to the development of safer therapies and improve the current CRISPR-based applications.
Key words: CRISPR-Cas9, PTM, ubiquitylation. has been shown to trigger apoptosis and restore sensitivity to chemotherapeutic chemicals. Evidence on the interplay of these effects with the biochemistry of liver cells is controversial. Therefore, we aimed to investigate the possible therapeutic effects of GT3 on liver cancer cell line using molecular biological techniques.

Materials and Methods:
In order to investigate the effects of combination therapy on growth characteristics of HepG2 cells, we utilized MTT assay. Combination index was calculated by CompuSyn and impact of single versus combined drug application was investigated using western blot analysis.

Abstract
Background/Aim: Tay-Sachs disease is one of the lysosomal storage disorder (LSD) caused by mutation in Hexa gene, encoding for the α subunit of lysosomal β-hexosaminidase A (HEXA), responsible for degradation of GM2. HEXA gene deficiency affects the central neurvous system owing to GM2 accumulation in lysosomes which causes neuronal death and progressive neurodegeneration in patients. Recently generated Hexa -/-Neu3 -/knockout mouse mimics neuropathological and clinical abnormalities of the classical early onset Tay-Sachs disease. As lysosomes have critical role in autophagy completion, many LSD show defect in autophagic flux and accumulation of autophagic substrates. In this study, we aimed whether accumulated GM2 causes autophagic flux alteration in different brain regions and fibroblasts from early onset Tay-Sachs disease mice model.
Results: Alterations of autophagic flux markers were detected in four brain region of early-onset Tay-Sachs disease mouse model. In particular, cerebellum and thalamus region of Hexa-/-Neu3-/-showed increased accumulation of autophagosomes and autophagic substrates. Interestingly, we observed that rapamycine induction in fibroblast from early-onset Tay-Sachs disease mouse model boosts the completion of autophagy flux.

Conclusion:
In this study we conclude that there is a clear impairment in the fusion of autophagosomes with lysosomes which results in accumulated autophagosomes and block of autophagic pathway in early onset Tay-Sachs disease mouse model.

Abstract
Background: Abiotic stress has a negative impact on plant metabolism and crop production. Seed priming is one of the most effective seed enhancement techniques that regulate the phases of germination by controlled hydration. Seed priming improves the germination by treating seeds with various agents. One possible mechanism for this is the cell cycle arrest in G2 phase, owing to priming agents with high osmotic potential. This allows seeds to activate their antioxidant defense mechanism and prepares the plant for future stress conditions. The objective of this study is to investigate the biochemical responses related to seed priming in Brachypodium distachyon under salt and drought stress.

Materials and Methods:
Seed priming was performed in B. distachyon (Bd-21 line) by three priming methods as hydropriming with distilled water, osmopriming with KNO 3 and hormonal priming with salicylic acid (SA) in varying concentrations. B. distachyon plants were exposed to salinity by irrigation with 320 mM NaCl solution and drought stress by water withholding for 12 days. Relative water content (RWC) and relative membrane permeability (RMP) were performed to observe the effect of seed priming on plant physiology. The activities of antioxidants such as catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD), and proline concentration for seed primed plants were determined under salinity and drought stress.
Results: Physiological analysis revealed that highest damage occurred in 3% KNO 3 and all SA primed plants under abiotic stress. The highest proline concentration was measured in 3% KNO 3 and 0.5 mM SA primed plants. All priming methods increased POD activity while decreased SOD activity.
However, CAT activity varied among priming methods.